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. 2018 Jun 25;9:810. doi: 10.3389/fpls.2018.00810

Table 5.

Putative loci differentially selected among northern and southern samples of wild Chinese chestnut, identified by comparing allele frequencies among pools of chestnut, with annotations based on the best UniProt alignments of predicted genes.

LGa Start End Nb Sc Sdd Predicted genee
LGA 72907000 72988000 0.56 087 >2 C94A2_VICSA: cytochrome P450, fatty acid oxidation
LGA 79800000 79880000 0.67 0.95 >3 Y2060_ARATH: BTB/POZ domain ubiquination protein
LGA 80300000 80330000 0.61 0.89 >3 SD25_ARATH: protein kinase
LGA 82239000 82355000 0.65 0.99 >4 PLY19_ARATH: pectate lyase 19
LGB 15342000 15410000 0.64 0.91 >3 E134_MAIZE: endo-1,3;1,4-beta-D-glucanase
LGB* 6540000 6678000 0.71 0.95 >3 SEOB_ARATH*, sieve-element occlusion protein
LGC 48510000 48811632 0.66 0.83 >2 SIB1_ARATH: sigma binding factor, pathogen defense
LGC* 50000000 50186000 0.69 0.95 >3 CNR2_MAIZE*, cell-number regulator
LGC 53870000 53947000 0.57 0.86 >3 PP413_ARATH: pentatricopeptide repeat-containing protein
LGE 16600000 16700000 0.67 1.00 >4 CCR1_ARATH: cinnamoyl-CoA reductase, lignin synthesis; Phytophthora cinammomi resistance?
LGG 43890000 43990000 0.70 0.99 >3 HMDH1_GOSHI: isoprenoid precursor (mevalonate) synthesis
LGG 48970000 49040000 0.61 0.88 >3 CPC_ARATH: trichome development transcription factor
LGI 4295000 4336000 0.62 0.89 >4 SILD_FORIN, ILR1_ARATH: lignin biosynthesis
LGL 58890000 59190000 0.69 0.97 >4 ERF25_ARATH, DRE1B_ARATH: cold tolerance
LGE 34000000 34100000 0.91 0.65 >3 CADH_EUCBO: cinnamoyl alcohol dehydrogenase, lignin synthesis
LGH 18500000 18547000 0.81 0.62 >3 SAG13_ARATH: senescence-associated protein

Gray shading indicates loci with evidence of directional selection in northern Chinese samples.

a

Average major allele frequency in northern Chinese wild trees for the given interval of 10 predicted genes;

b

Average major allele frequency in southern Chinese wild trees for the given interval of 10 predicted genes;

c

Standard deviations greater than the average difference in major allele frequency between orchard and wild pools.

d

Standard deviations from mean difference in allele frequency between northern and southern pools;

e

Annotation of predicted chestnut gene (AUGUSTUS) based on alignment to the UniProtKB/Swiss-Prot database.

*

Also identified as putative domestication loci due to low Tajima's D-value in orchard samples.